Medicaid and SCHIP Improvement and Flexibility Act of 2000 - Amends titles XIX (Medicaid) and XXI (State Children's Health Insurance Program) (SCHIP) of the Social Security Act (SSA) to mandate: (1) development and use of a uniform, simplified application form for establishing eligibility for Medicaid and SCHIP benefits; and (2) coordinated enrollment processes.

(Sec. 2) Provides for the expanded availability of funding for administrative costs related to certain outreach and eligibility determinations under Medicaid and SCHIP with regard to children and pregnant women.

Directs the Secretary to establish a procedure with regard to the participation of local and community-based public or nonprofit organizations in outreach and enrollment activities if States do not otherwise obligate the amounts made available under this Act.

Sets forth a special rule for certain enrollment and outreach activities providing for use of three percent of SCHIP funds at a 90 percent Federal match for such activities.

Amends SSA title XIX to provide for additional entities (including elementary and secondary schools, child support enforcement agencies, and child care resource and referral agencies) that are qualified to determine Medicaid presumptive eligibility for low-income children.

(Sec. 3) Amends SSA title XXI to require a State health plan, to the extent it provides coverage other than under the State's Medicaid plan, to provide a three-month grace period before disenrollment for nonpayment of premiums, as well as an opportunity for a hearing on the matter.

Prohibits State child health plan eligibility standards from permitting the use of mandatory waiting periods, unless the Secretary finds that such a period would not be contrary to title XXI.

(Sec. 4) Amends SSA title XIX to provide for: (1) automatic reassessment of eligibility for SCHIP and Medicaid benefits for children losing Medicaid or SCHIP eligibility; (2) optional SCHIP coverage of low-income, uninsured pregnant women; (3) State option to cover qualified alien children under the Medicaid and SCHIP programs; (4) elimination of the funding offset for exercise of the presumptive eligibility option; (5) automatic enrollment of children born to targeted low-income pregnant women receiving pregnancy-related assistance under such programs; and (6) SCHIP and Medicaid program coordination with the Maternal and Child Health Services program under SSA title V.

(Sec. 5) Provides that amounts allotted to a State under SCHIP under the three-year availability of amounts allotted for FY 1998 and 1999 shall remain available through September 30, 2002.

(Sec. 6) Amends SSA title XXI for the stated purpose of permitting an increased share of SCHIP funds to be expended for prevention programs that ensure healthy childhoods and quality prenatal health care.

(Sec. 7) Amends SSA title XIX for the stated purpose of providing for the use of SCHIP funds for an enhanced matching rate for coverage of additional children under Medicaid.